NM_001025195.2:c.955delC
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001025195.2(CES1):c.955delC(p.Leu319PhefsTer5) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,613,924 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00023 ( 0 hom. )
Consequence
CES1
NM_001025195.2 frameshift
NM_001025195.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.38
Genes affected
CES1 (HGNC:1863): (carboxylesterase 1) This gene encodes a member of the carboxylesterase large family. The family members are responsible for the hydrolysis or transesterification of various xenobiotics, such as cocaine and heroin, and endogenous substrates with ester, thioester, or amide bonds. They may participate in fatty acyl and cholesterol ester metabolism, and may play a role in the blood-brain barrier system. This enzyme is the major liver enzyme and functions in liver drug clearance. Mutations of this gene cause carboxylesterase 1 deficiency. Three transcript variants encoding three different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.955delC | p.Leu319PhefsTer5 | frameshift_variant | Exon 9 of 14 | ENST00000360526.8 | NP_001020366.1 | |
CES1 | NM_001025194.2 | c.952delC | p.Leu318PhefsTer5 | frameshift_variant | Exon 9 of 14 | NP_001020365.1 | ||
CES1 | NM_001266.5 | c.952delC | p.Leu318PhefsTer5 | frameshift_variant | Exon 9 of 14 | NP_001257.4 | ||
CES1 | XM_005255774.3 | c.955delC | p.Leu319PhefsTer5 | frameshift_variant | Exon 9 of 14 | XP_005255831.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152164Hom.: 0 Cov.: 34
GnomAD3 genomes
AF:
AC:
46
AN:
152164
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000225 AC: 329AN: 1461642Hom.: 0 Cov.: 33 AF XY: 0.000223 AC XY: 162AN XY: 727122
GnomAD4 exome
AF:
AC:
329
AN:
1461642
Hom.:
Cov.:
33
AF XY:
AC XY:
162
AN XY:
727122
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000302 AC: 46AN: 152282Hom.: 0 Cov.: 34 AF XY: 0.000416 AC XY: 31AN XY: 74480
GnomAD4 genome
AF:
AC:
46
AN:
152282
Hom.:
Cov.:
34
AF XY:
AC XY:
31
AN XY:
74480
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
5
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
DRUG METABOLISM, ALTERED, CES1-RELATED Uncertain:1
May 17, 2023
Department of Pathology and Laboratory Medicine, Sinai Health System
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: research
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at